Simulating DNA at low resolution

The past year has witnessed the development of several new mathematical approaches to analyzing the structure of double-helical DNA and to incorporating the sequence-dependent features of the chain in computer simulations of long polymers. Of special interest in this respect are the local and global structural changes induced by the binding of various proteins to DNA, ranging from subtle bending, untwisting and sliding motions at the base-pair level to the apparent organization of supercoiled structure in chains that are thousands of residues long. The computational effort has also included both new ways to incorporate the polyelectrolyte character of DNA and other environmental forces in simulations of long chains and new methods to keep track of the multitude of configurations so generated. The collective advances are pointing to ways that will soon connect the sequences of base pairs in large genomes to folded three-dimensional structures based on natural bending, twisting and translational tendencies and in response to deformations produced by the binding of different proteins.